GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aspS2 in Escherichia coli BW25113

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate 15054 b0930 asparaginyl-tRNA synthetase (NCBI)

Query= curated2:Q8TXG4
         (431 letters)



>FitnessBrowser__Keio:15054
          Length = 466

 Score =  179 bits (455), Expect = 1e-49
 Identities = 137/453 (30%), Positives = 217/453 (47%), Gaps = 58/453 (12%)

Query: 18  EVRLAGWVHEVRDL-GGIKFVLLRDRT------GIVQLTLPKQKVPKETFEKVPKLTKES 70
           EV + GWV   RD   GI F+ + D +       ++  +LP         E V +LT   
Sbjct: 19  EVTVRGWVRTRRDSKAGISFLAVYDGSCFDPVQAVINNSLPNYN------EDVLRLTTGC 72

Query: 71  VIRVEGTVQANEKAPGGVEVIPQRIEV---LSESDTHLPLDPTGKVDADLDTRLDARVLD 127
            + V G V A+       E+   ++EV   + + DT+    P       ++   +   L 
Sbjct: 73  SVIVTGKVVASPGQGQQFEIQASKVEVAGWVEDPDTY----PMAAKRHSIEYLREVAHLR 128

Query: 128 LRREEPQAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV-------- 179
            R     A+ ++R+ +  A+  F  E+GF  V TP I AS TEG  E+F V         
Sbjct: 129 PRTNLIGAVARVRHTLAQALHRFFNEQGFFWVSTPLITASDTEGAGEMFRVSTLDLENLP 188

Query: 180 ------------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEA 227
                       +F ++++L  S QL  +   A    ++Y  GP FRAE  NT RHL E 
Sbjct: 189 RNDQGKVDFDKDFFGKESFLTVSGQLNGETY-ACALSKIYTFGPTFRAENSNTSRHLAEF 247

Query: 228 ISVDIEMSFIESEEDVMRVLEELLAHVFRKVREECEKEL---------EALDRELPELET 278
             ++ E++F     D+  + E +L +VF+ V EE   ++         +A+ R    +E 
Sbjct: 248 WMLEPEVAFANLN-DIAGLAEAMLKYVFKAVLEERADDMKFFAERVDKDAVSRLERFIEA 306

Query: 279 PFERITYEETLDLLSEHGIEVE----WGEDLPTEAERKLGEI-FEEPFFITEWPRETRPF 333
            F ++ Y + + +L   G + E    WG DL +E ER L E  F+ P  +  +P++ + F
Sbjct: 307 DFAQVDYTDAVTILENCGRKFENPVYWGVDLSSEHERYLAEEHFKAPVVVKNYPKDIKAF 366

Query: 334 YTMAKDDEVTTA-FDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKY 391
           Y    +D  T A  D++  G+ E+  G+QRE R DVL  ++ E GL+ ED+  Y +  +Y
Sbjct: 367 YMRLNEDGKTVAAMDVLAPGIGEIIGGSQREERLDVLDERMLEMGLNKEDYWWYRDLRRY 426

Query: 392 GMPPHGGWGLGLERTLMTITGAENIREVTLFPR 424
           G  PH G+GLG ER +  +TG +N+R+V  FPR
Sbjct: 427 GTVPHSGFGLGFERLIAYVTGVQNVRDVIPFPR 459


Lambda     K      H
   0.318    0.138    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 486
Number of extensions: 32
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 431
Length of database: 466
Length adjustment: 33
Effective length of query: 398
Effective length of database: 433
Effective search space:   172334
Effective search space used:   172334
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory